The Ellis started life as the CSS Ellis when she was purchased by the state of North Carolina in 1861 at Norfolk, Virginia and turned over to the Confederacy. She was placed under the command of Commander W T Muse, and sat to the defense of Fort Hatteras in North Carolina. On February 10th 1862 she was taken by the Union after a desperate fight with the USS Ceres just off of Elizabeth City, North Carolina.She then became the USS Ellis and as part of the Union Navy was assigned to the North Atlantic Blocking Squadron. Under the command of Lieutenant C L Franklin she went into service in the rivers of the North Carolina coast. The Ellis took part in the capture of Fort Macon on April 25th 1862, and destroyed a battery and salt works at Swansboro, North Carolina in August 1862.
The Ellis sailed up the New River Inlet in November 1862 under the command of Lieutenant William B Cushing. She captured two Confederate schooners, but ran aground on November 24th 1862 as she sailed back down the river. After dark Cushing had all of the Ellis’ equipment, guns, coal, and all but five crew members transferred to the captured schooners. As the schooners went down the river Cushing and his five crewmen waited on the Ellis for a fight. In the early hours of November 25th 1862 the Confederates opened fire on the Ellis. Cushing refused to surrender his ship, so before leaving her he had fires set on board, and the one remaining gun loaded and pointed toward the Confederates so it would shoot when the fire reached it. The Ellis blew up shortly after she was abandoned when the fires exploded her magazine.Cushing and his men made their escape to the schooners and out the mouth of the inlet.